rs2303191
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_016373.4(WWOX):c.516+6T>C variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.732 in 1,612,444 control chromosomes in the GnomAD database, including 433,805 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.75 ( 43510 hom., cov: 31)
Exomes 𝑓: 0.73 ( 390295 hom. )
Consequence
WWOX
NM_016373.4 splice_donor_region, intron
NM_016373.4 splice_donor_region, intron
Scores
2
Splicing: ADA: 0.0002358
2
Clinical Significance
Conservation
PhyloP100: -1.92
Genes affected
WWOX (HGNC:12799): (WW domain containing oxidoreductase) This gene encodes a member of the short-chain dehydrogenases/reductases (SDR) protein family. This gene spans the FRA16D common chromosomal fragile site and appears to function as a tumor suppressor gene. Expression of the encoded protein is able to induce apoptosis, while defects in this gene are associated with multiple types of cancer. Disruption of this gene is also associated with autosomal recessive spinocerebellar ataxia 12. Disruption of a similar gene in mouse results in impaired steroidogenesis, additionally suggesting a metabolic function for the protein. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
Variant 16-78164295-T-C is Benign according to our data. Variant chr16-78164295-T-C is described in ClinVar as [Benign]. Clinvar id is 260739.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-78164295-T-C is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.883 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WWOX | NM_016373.4 | c.516+6T>C | splice_donor_region_variant, intron_variant | ENST00000566780.6 | |||
WWOX | NM_001291997.2 | c.177+6T>C | splice_donor_region_variant, intron_variant | ||||
WWOX | NM_130791.5 | c.516+6T>C | splice_donor_region_variant, intron_variant | ||||
WWOX | NR_120436.3 | n.755+6T>C | splice_donor_region_variant, intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WWOX | ENST00000566780.6 | c.516+6T>C | splice_donor_region_variant, intron_variant | 1 | NM_016373.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.754 AC: 114579AN: 151990Hom.: 43457 Cov.: 31
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GnomAD3 exomes AF: 0.748 AC: 185664AN: 248274Hom.: 69863 AF XY: 0.741 AC XY: 99764AN XY: 134646
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GnomAD4 exome AF: 0.730 AC: 1065815AN: 1460336Hom.: 390295 Cov.: 36 AF XY: 0.728 AC XY: 528886AN XY: 726428
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GnomAD4 genome AF: 0.754 AC: 114691AN: 152108Hom.: 43510 Cov.: 31 AF XY: 0.753 AC XY: 55990AN XY: 74348
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ClinVar
Significance: Benign
Submissions summary: Benign:7
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 07, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Jul 15, 2024 | This variant is classified as Benign based on local population frequency. This variant was detected in 97% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy and Progressive Myoclonus Epilepsy. Number of patients: 90. Only high quality variants are reported. - |
Autosomal recessive spinocerebellar ataxia 12;C3463992:Developmental and epileptic encephalopathy, 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Developmental and epileptic encephalopathy, 28 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Apr 20, 2017 | - - |
Autosomal recessive spinocerebellar ataxia 12 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at